Saturday, September 30, 2006

Researching the literature is an essential part of every research project. Much of this can be done on the internet where Google Scholar, Pubmed, CiteSeer or similar services can help in finding relevant information. The next step is managing all the articles you have found. For this, I use Reference Manager but there are many other desktop applications for the task at hand. But wouldn't it be great to move this part of the process on the internet as well instead of switching to a desktop application?

Connotea (www.connotea.org) and CiteULike (www.citeulike.org) claim to offer exactly this. Both are collaborative tagging systems with a focus on scientists who want to share, store and organize academic papers.

CiteULike is provided Richard Cameron and generously hosted by the University of Manchester in England. Connotea was created by Nature publishing group. Both services are free to everyone. Registration is simple and no personal information is needed. I am not sure if CiteULike is still actively developed (because the bug tracking system is full of spam and the search function on the site doesn't work at all).

Input of articles

Both services make use of "bookmarklets" which start a JavaScript to analyze the current page in the browser. When you see a paper or a book on the web that interests you, you can click one button, the bibliographic information is extracted and added to your personal library. This works well for various publishers’ webpages. The Citeulike site stores the bibliographic info, including the abstract. Connotea, on the other hand, is literally a bookmarking system. The DOI is the primary identification info. It gets interesting when you try to post bibliographic information manually, i.e. print-only articles. You can manually enter detailed biblio info to CiteULike (but curiously missing are DOI and ISSN fields). In Connotea, you can only post an URL, and a title. There is no way to add the full reference, unless there is a DOI for the article. This means that it is not possible to input articles that are older than 10 years or so. (see comments) Although even an article from 1771 has been issued a DOI, there are very few articles older than 10 years which bear a DOI (i.e. in comparison to all the scientific articles that have been published). But especially in taxonomy all that "old stuff" is still important and wants to be cited. This makes Connotea more or less useless for my purposes.

Organizing your articles

Organization of articles in your library is mainly based on tags. Sorting of articles in your library or articles for a specific tag is always based on the date of posting. I am missing other sorting options (author name, date of publication, ...) and I would like the control the display of entries. CiteULike automatically tags author names and Livesearch by authors or tags of your library is very fast. Both systems let you add notes to your articles and in CiteULike you can even attach personal PDF copies.

Sharing & exploring articles

Connotea and CiteULike let you search through everyone's libraries (although the search in CiteULike seems to be broken). For each paper in your library it is displayed which other users have it in their libraries. I would like some more features to find "interesting stuff", e.g. popular articles by tag (see del.icio.us for how to do it).

Both systems have "groups" which are totally useless. If you belong to group everything you post will show up in that group. The core of a group is a shared interest on a topic area, but a user may have many interests. Therefore you should be able to decide which paper in your library you want to share with a particular group.

In CiteULike metadata of references that were manually added are not shared with other users. That means search results will not output any of these references even if you entered these yourself and you are logged into your account. This should be some kind of protection against spam but turns out to be an unacceptable feature.

Connotea lets you build a profile page. Nice.

Exporting articles

CiteULike allows you to export your collected references in BitTex and Endnote format. The options for export in Connotea are extensive: RIS, Endnote, BibTex and XML. I haven't tested any of these.

Both systems also allow syndication of your library as RSS. This is potentially a great option to keep an eye (via a feed reader) on interesting articles that other users add to Connotea or CiteULike. I am especially interested in connecting the collected references in CiteULike or Connotea with my website (www.ants-cachoeira.net) via RSS. Unfortunately, CiteULike omits some information (authors !) in the RSS feed and Connotea has by design an even more limited subset of needed information. I have experimentally included a list of references, which are linked via RSS to tagged references in my CiteULike library on my page on Amblyopone (scroll down to section: Offline references for Amblyopone). As you can see an important piece of bibliographic information is missing: the author(s). I do not understand why you would include the full abstract of an article in an RSS feed but not the author(s). The bibliographic information given in the RSS from Connotea is even more basic and does not include authors nor journal information.

Wishlist for a better system

Include full bibliographic information in the RSS feed and/or offer a tool for displaying collected bibliographies on other places on the web (e.g. linkrolls in del.icio.us).

Let me control the sorting and display of entries of my library.

(Connotea) Give me the possibility to include print-only papers in my library (with full bibliographic information).

Add some real group features where I can decide which paper to include in the group.

In my view CiteULike is much nearer the desired tool than Connotea which offers few additional features to del.icio.us with a less powerful user interface. You may want to share your experience with CiteULike or Connotea by commenting this entry.

84 comments:

Anonymous
said...

Hi Jochen:

Just to point out that DOI is not restricted to online material only in any way, shape or form (although inevitably tends to be used for these materials). Anyhows, DOI's have been issued across more than 10 years. CrossRef have an instance going back to 1771, see:

Thanks for the clarification about DOIs. Interesting fact that even an article from 1771 has been assigned a DOI. I was wrong that only articles from the last years have been issued a DOI. Nevertheless this is a rare exception, e.g. for the ca. 3800 taxonomic publications on ants databased at antbase.org / Hymenoptera Name Server only a very small minority have been issued DOIs. Donat Agosti counted that these were published in about 400 (often obscure) journals. I doubt that much of this "old stuff" will get a DOI in the forseeable future.

Another tool you might find interesting is www.postgenomic.com. It collects information on science blogs, paper reviews, conferences, data. Have a look in the wiki section to find out how to connect it with pubmed.

Connotea has some nice features, such as RSS feeds as RDF, which make it easy to download and play with the bibliography. It also has a nice API. As an example of what can be done, I've described a tool for taking uBio's list of ant papers (the feed you show on your blog) and add the papers to Connotea (with some additional annotations from uBio and Yahoo). Regarding the lack of online publications, they could go into Connoea without a DOI, so long as there is a URL, and this would be fairly easy to do.

Connotea has indeed some nice features and the open API is a special treat for developers. The tool you created is a great example what can be done with Connotea.Nevertheless, even a RSS feed as RDF is useless (regarding Connotea as a bibliographic tool) as long as the feed does not include information about the authors.Creating an url for an offline publication is definitely no solution for the lack of Connotea to accept print only publications. This work-around is much too time-consuming for being useful. Why not let users input offline publications like CiteULike does? I see Connotea as bibliographic tool in the first place and not merely as a database (for that I prefer delcious).

Interesting article. I note that you say "...But wouldn't it be great to move this part of the process on the internet as well instead of switching to a desktop application?"Have you looked at RefWorks (www.refworks.com)? OK...full disclosure...I am with RefWorks. But it is the first and leading application that manages bibliographic information on the web.

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